Contacts of the helix formed by residues 191 - 199 (chain D) in PDB entry 4PEI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B PRO* 4.6 19.2 - - - +
190D GLY* 1.3 68.1 - - - -
192D TYR* 1.3 55.7 + - - +
193D LYS* 3.4 10.6 + - - +
194D GLN* 3.1 38.5 + - + +
195D LEU* 3.0 22.3 + - - +
197D ARG* 5.7 1.4 - - - +
235D TYR* 3.4 11.2 + - + -
236D HIS 4.5 1.4 + - - -
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Residues in contact with TYR 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D VAL* 3.6 18.8 - - + +
188D MET* 3.5 49.7 - - + +
190D GLY 2.9 20.4 + - - -
191D ASN* 1.3 71.2 - - - +
193D LYS* 1.3 85.9 + - + +
195D LEU* 3.6 8.3 - - - -
196D TYR* 2.9 63.6 + + + +
235D TYR* 3.7 4.3 - - - +
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Residues in contact with LYS 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LYS 5.8 1.8 + - - -
191D ASN* 3.0 8.9 + - - +
192D TYR* 1.3 105.3 + - + +
194D GLN* 1.3 66.1 + - - +
196D TYR* 3.2 8.7 + - + +
197D ARG* 2.9 44.4 + - - +
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Residues in contact with GLN 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B SER* 3.6 24.2 + - - -
30B GLU* 5.6 1.6 - - - +
82B TYR* 5.6 1.0 + - - -
191D ASN* 3.1 34.7 + - + +
193D LYS* 1.3 77.5 - - - +
195D LEU* 1.3 60.5 + - - +
197D ARG* 3.0 49.7 - - - +
198D PHE* 3.2 47.7 + - + -
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Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D TRP* 4.2 7.0 - - + -
187D VAL* 3.5 31.6 - - + -
191D ASN 3.0 9.6 + - - +
192D TYR* 3.7 4.9 - - - +
193D LYS 3.1 0.2 - - - -
194D GLN* 1.3 78.3 - - - +
196D TYR* 1.3 65.1 + - + +
198D PHE* 3.1 7.2 + - + -
199D GLN* 2.9 31.8 + - + +
202D PHE* 3.9 26.5 - - + -
233D CYS* 4.1 23.8 - - + -
234D GLU 4.6 2.2 - - - +
235D TYR* 3.6 36.8 - - + -
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Residues in contact with TYR 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D VAL* 4.2 8.5 - - + +
188D MET* 4.1 12.4 - - + -
192D TYR* 2.9 44.5 + + + +
193D LYS* 3.2 8.7 + - + +
195D LEU* 1.3 87.1 - - + +
197D ARG* 1.3 64.5 + - - +
199D GLN 3.7 4.7 - - - -
200D PRO* 3.3 24.9 - - - +
202D PHE* 3.9 15.2 + - + -
203D LYS* 3.5 63.0 - - + +
206D GLY* 3.5 27.8 + - - -
209D LEU* 5.9 0.9 - - + -
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Residues in contact with ARG 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B SER* 5.7 0.8 + - - -
191D ASN* 5.7 0.8 - - - +
193D LYS* 2.9 39.8 + - - +
194D GLN* 3.0 47.2 - - - +
196D TYR* 1.3 79.0 - - - +
198D PHE* 1.3 67.8 + - + +
200D PRO* 4.3 8.0 - - - +
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Residues in contact with PHE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 4.6 35.0 - - + -
194D GLN* 3.2 50.0 + - + +
195D LEU* 3.1 7.2 + - + +
197D ARG* 1.3 87.7 - - + +
199D GLN* 1.3 83.9 + - + +
200D PRO* 3.6 6.9 - - - +
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Residues in contact with GLN 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LEU* 2.9 18.0 + - + +
196D TYR* 3.6 8.1 - - - +
198D PHE* 1.3 103.1 + - + +
200D PRO* 1.3 62.6 - - - +
201D GLY 2.8 12.4 + - - -
202D PHE* 2.9 59.1 + - + +
203D LYS 4.0 0.3 + - - -
232D HIS 3.8 18.7 + - - +
233D CYS* 4.4 8.5 - - + +
254D ASN* 6.0 0.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il